Variant report

Variant	rs11577797
Chromosome Location	chr1:239574661-239574662
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 23 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs10802766	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10802767	0.94[ASN][1000 genomes]
rs10925879	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10925880	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10925886	0.84[ASN][1000 genomes]
rs12124516	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12129794	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12133100	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4617391	0.81[ASN][1000 genomes]
rs60146392	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6662827	0.84[ASN][1000 genomes]
rs6678395	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7519061	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7541385	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1002301	chr1:239182255-239774393	Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv1006640	chr1:239290853-239658788	Active TSS Bivalent Enhancer Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	nsv535358	chr1:239290853-239658788	Weak transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	nsv549435	chr1:239375010-239974006	Active TSS Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
5	nsv873349	chr1:239475925-239587512	Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Weak transcription Bivalent/Poised TSS Bivalent Enhancer Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
6	esv3373454	chr1:239495349-239670615	Bivalent Enhancer Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
7	nsv873350	chr1:239498915-239648140	Enhancers Bivalent/Poised TSS Bivalent Enhancer Active TSS Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
8	nsv833037	chr1:239522168-239699412	Enhancers Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Active TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
9	esv3383016	chr1:239574235-239576242	Weak transcription Flanking Active TSS Enhancers Strong transcription	n/a	n/a	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11577797	TBCE	cis	parietal	SCAN
rs11577797	IRF2BP2	cis	cerebellum	SCAN

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:239570600-239581400	Weak transcription	Ovary	ovary
2	chr1:239572200-239577400	Weak transcription	Pancreas	Pancrea
3	chr1:239572800-239581400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
4	chr1:239573400-239574800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr1:239573800-239574800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
6	chr1:239573800-239574800	Enhancers	Fetal Stomach	stomach
7	chr1:239574400-239574800	Enhancers	Colon Smooth Muscle	Colon
8	chr1:239574400-239576200	Weak transcription	Fetal Intestine Small	intestine
9	chr1:239574600-239577000	Weak transcription	Stomach Smooth Muscle	stomach
10	chr1:239574600-239577200	Weak transcription	Cortex derived primary cultured neurospheres	brain
11	chr1:239574600-239577200	Weak transcription	Rectal Smooth Muscle	rectum
12	chr1:239574600-239577400	Weak transcription	Primary hematopoietic stem cells	blood

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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